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Conserved domains on  [gi|1425384578|gb|RBS28082|]
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RNA polymerase sigma-70 factor [Enterococcus faecium]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08295 super family cl32289
RNA polymerase sporulation sigma factor SigH;
3-187 1.28e-20

RNA polymerase sporulation sigma factor SigH;


The actual alignment was detected with superfamily member PRK08295:

Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 84.96  E-value: 1.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGVSFGSYYKSIISNQIYS 82
Cdd:PRK08295   12 EELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIIT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  83 LLRKQNALKRRDQKDEVSIDQKIETEGPD-FL------AEITLQEPLAIQHLLLKEAIENCEIQFSKIEAKIFHYYMQGV 155
Cdd:PRK08295   92 AIKTANRQKHIPLNSYVSLDKPIYDEESDrTLldviseAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYLDGK 171

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1425384578 156 DFVDMAECLAMDHKQVMSAYGRVKLKIKKHLK 187
Cdd:PRK08295  172 SYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
3-187 1.28e-20

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 84.96  E-value: 1.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGVSFGSYYKSIISNQIYS 82
Cdd:PRK08295   12 EELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIIT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  83 LLRKQNALKRRDQKDEVSIDQKIETEGPD-FL------AEITLQEPLAIQHLLLKEAIENCEIQFSKIEAKIFHYYMQGV 155
Cdd:PRK08295   92 AIKTANRQKHIPLNSYVSLDKPIYDEESDrTLldviseAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYLDGK 171

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1425384578 156 DFVDMAECLAMDHKQVMSAYGRVKLKIKKHLK 187
Cdd:PRK08295  172 SYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 3-187 5.31e-17

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 74.65  E-value: 5.31e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRlkntyYLRNYV-----SEDWEQEARIALYQALRTYEKSKgvSFGSYYKSIIS 77
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYR-----YARRLLgdradAEDLVQETFLRLWRKLDSFRGRG--SFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  78 NQIYSLLRKQNalKRRDQKDEVSIDQKIETEGPDFLAEitlqepLAIQHLLLKEAIEnceiQFSKIEAKIFH-YYMQGVD 156
Cdd:COG1595    78 NLAIDHLRKRR--RRRELLDELAEELPDEAADPEEALE------AEELLEALLAALE----RLPPRQREVLVlRYLEGLS 145

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1425384578 157 FVDMAECLAMDHKQVMSAYGRVKLKIKKHLK 187
Cdd:COG1595   146 YAEIAEILGISEGTVKSRLSRARKKLREALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-186 1.83e-12

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 61.98  E-value: 1.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  15 EAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKgvSFGSYYKSIISNQIYSLLRKQNALKRRD 94
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  95 QKDEvsidqkietEGPDFLAEITLQEPLAIQHLLLKEAIENCEIQFSKIeakIFHYYMQGVDFVDMAECLAMDHKQVMSA 174
Cdd:TIGR02937  79 DLLE---------ELLDSDPSPEEELEQEEEREALREALEKLPEREREV---LVLRYLEGLSYKEIAEILGISVGTVKRR 146

                         170
                  ....*....|..
gi 1425384578 175 YGRVKLKIKKHL 186
Cdd:TIGR02937 147 LKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 20-88 1.47e-10

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 54.90  E-value: 1.47e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1425384578  20 LYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGVSFGSYYKSIISNQIYSLLRKQN 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
3-187 1.28e-20

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 84.96  E-value: 1.28e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGVSFGSYYKSIISNQIYS 82
Cdd:PRK08295   12 EELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIIT 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  83 LLRKQNALKRRDQKDEVSIDQKIETEGPD-FL------AEITLQEPLAIQHLLLKEAIENCEIQFSKIEAKIFHYYMQGV 155
Cdd:PRK08295   92 AIKTANRQKHIPLNSYVSLDKPIYDEESDrTLldviseAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLELYLDGK 171

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1425384578 156 DFVDMAECLAMDHKQVMSAYGRVKLKIKKHLK 187
Cdd:PRK08295  172 SYQEIAEELNRHVKSIDNALQRVKRKLEKYLE 203
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 3-187 5.31e-17

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 74.65  E-value: 5.31e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRlkntyYLRNYV-----SEDWEQEARIALYQALRTYEKSKgvSFGSYYKSIIS 77
Cdd:COG1595     5 EELLERLRAGDEAAFEELYERYRPRLYR-----YARRLLgdradAEDLVQETFLRLWRKLDSFRGRG--SFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  78 NQIYSLLRKQNalKRRDQKDEVSIDQKIETEGPDFLAEitlqepLAIQHLLLKEAIEnceiQFSKIEAKIFH-YYMQGVD 156
Cdd:COG1595    78 NLAIDHLRKRR--RRRELLDELAEELPDEAADPEEALE------AEELLEALLAALE----RLPPRQREVLVlRYLEGLS 145

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1425384578 157 FVDMAECLAMDHKQVMSAYGRVKLKIKKHLK 187
Cdd:COG1595   146 YAEIAEILGISEGTVKSRLSRARKKLREALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 15-186 1.83e-12

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 61.98  E-value: 1.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  15 EAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKgvSFGSYYKSIISNQIYSLLRKQNALKRRD 94
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRRLRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  95 QKDEvsidqkietEGPDFLAEITLQEPLAIQHLLLKEAIENCEIQFSKIeakIFHYYMQGVDFVDMAECLAMDHKQVMSA 174
Cdd:TIGR02937  79 DLLE---------ELLDSDPSPEEELEQEEEREALREALEKLPEREREV---LVLRYLEGLSYKEIAEILGISVGTVKRR 146

                         170
                  ....*....|..
gi 1425384578 175 YGRVKLKIKKHL 186
Cdd:TIGR02937 147 LKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 20-88 1.47e-10

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 54.90  E-value: 1.47e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1425384578  20 LYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGVSFGSYYKSIISNQIYSLLRKQN 88
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 3-107 2.33e-07

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 49.05  E-value: 2.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLknTYYLRNYVSEDWE---QEARIALYQALRTYEKSKGVSFGSYYKSIISNQ 79
Cdd:COG1191     3 EELLRRYQEGDEEAREELIEEYLPLVKKI--ASRLAGRLPAELDdliQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                          90       100
                  ....*....|....*....|....*...
gi 1425384578  80 IYSLLRKQNALKRRDQKDEVSIDQKIET 107
Cdd:COG1191    81 ILDYLRDEDWVPRSVRELARKIEEAIEE 108
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 3-110 2.61e-06

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 45.78  E-value: 2.61e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYekSKGVSFGSYYKSIISNQIYS 82
Cdd:PRK09638    6 KELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSF--QGRSKFSTWLISIASRLYKD 83

                          90       100       110
                  ....*....|....*....|....*....|
gi 1425384578  83 LLRKQNALKRRDQ--KDEVSIDQKIETEGP 110
Cdd:PRK09638   84 HLRKQKREKLRLQraKEETLRKEKWEAAIK 113
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 6-135 4.22e-05

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 42.10  E-value: 4.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   6 LRAARNGDEEAFAALYQKYFPLLLRlkntyYLRNYVS-----EDWEQEARIALYQALRTYEksKGVSFGSYYKSIISNQI 80
Cdd:PRK09652    1 VERVQRGDRAAFALLVRRYQPRVKR-----LLSRLTRdpadaEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTA 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1425384578  81 YSLLRKQnalKRRDQKDEVSIDQKIETEGPDFLAEITLQEPLAIQHLL---LKEAIEN 135
Cdd:PRK09652   74 INYLRKQ---GRRPPASDVDAEEAEDFDLADALRDISTPENELLSAELeqrVRAAIES 128
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
3-88 1.23e-04

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 41.39  E-value: 1.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTyYLRNYVseDWEQE-----ARIALYQALRTYEKSKGVSFGSYYKSIIS 77
Cdd:PRK08311    6 EDILEKIKNGDEELREELIEEYKPFIAKVVSS-VCGRYI--DWENDdelsiGLIAFNEAIDSYDEEKGKSFLSFAELVIK 82

                          90
                  ....*....|.
gi 1425384578  78 NQIYSLLRKQN 88
Cdd:PRK08311   83 RRLIDYFRKES 93
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 3-65 3.82e-04

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 39.51  E-value: 3.82e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKG 65
Cdd:PRK13919   11 EALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG 73
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 3-186 1.57e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 37.71  E-value: 1.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKYFPLLLRLKnTYYLRNYV-SEDWEQEARIALYQALRTYeKSKGVSFGSYYKSIISNQIY 81
Cdd:PRK05602    8 EELLARVAAGDPAAFRVLVARKLPRLLALA-TRMLGDPAeAEDVAQETFLRIWKQAPSW-RPGEARFDTWLHRVVLNLCY 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578  82 SLLRkqnalKRRDQKDEVSIDQKIETEGPDFLAEITLQEPLAIQHLLL-----KEAIENCeiqfskieakifhyYMQGVD 156
Cdd:PRK05602   86 DRLR-----RRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAAlperqREAIVLQ--------------YYQGLS 146

                         170       180       190
                  ....*....|....*....|....*....|
gi 1425384578 157 FVDMAECLAMDHKQVMSAYGRVKLKIKKHL 186
Cdd:PRK05602  147 NIEAAAVMDISVDALESLLARGRRALRAQL 176
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 3-127 2.94e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 36.98  E-value: 2.94e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1425384578   3 EELLRAARNGDEEAFAALYQKY----FPLLLRLKNtyylRNYVSEDWEQEARIALYQALRTYEKSkgVSFGSYYKSIISN 78
Cdd:PRK12513   14 EALMLRYRAGDAAAFEALYARHrtglYRFLLRLAR----DRALAEDIFQETWLRVIRARAQYQPR--ARFRTWLYQIARN 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1425384578  79 QIYSLLRKQNAlkRR---DQKDEVSIDQKIETEGPDFLAEITLQEP---LAIQHL 127
Cdd:PRK12513   88 LLIDHWRRHGA--RQapsLDADEQLHALADDGAAPEQQLSLFRDRRrlqAALETL 140
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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